magic() function error: Stuck on "Calculating PCA..."

[StefanosVoglis]

Hello,
related to this issue #118:

unfortunately I keep getting a similar error. Once I call the magic function it sais "Calculating PCA" and then the R session crashes after a while.

> library(Rmagic) 
> library(reticulate) 
> py_config() 
python:         /home/rstudio/.local/share/r-miniconda/envs/r-reticulate/bin/python 
libpython:      /home/rstudio/.local/share/r-miniconda/envs/r-reticulate/lib/libpython3.8.so 
pythonhome:     /home/rstudio/.local/share/r-miniconda/envs/r-reticulate:/home/rstudio/.local/share/r-miniconda/envs/r-reticulate 
version:        3.8.16 \| packaged by conda-forge \| (default, Feb  1 2023, 16:01:55)  [GCC 11.3.0] 
numpy:          /home/rstudio/.local/lib/python3.8/site-packages/numpy 
numpy_version:  1.24.2 
> Rmagic::pymagic_is_available() 
[1] TRUE 
> data(magic_testdata)
> data_magic <- magic(magic_testdata, npca=ncol(magic_testdata)-1, genes=c("VIM", "CDH1", "ZEB1"))
Calculating MAGIC...
  Running MAGIC on 500 cells and 197 genes.
  Calculating graph and diffusion operator...
    Calculating PCA...

Any ideas what the reason could be?

Kind regards,

sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] reticulate_1.28 Rmagic_2.0.3 Matrix_1.5-3

loaded via a namespace (and not attached):
[1] bitops_1.0-7 matrixStats_0.63.0 EBImage_4.40.0 RColorBrewer_1.1-3
[5] rprojroot_2.0.3 GenomeInfoDb_1.34.9 tools_4.2.1 utf8_1.2.3
[9] R6_2.5.1 svgPanZoom_0.3.4 HDF5Array_1.26.0 vipor_0.4.5
[13] BiocGenerics_0.44.0 colorspace_2.1-0 rhdf5filters_1.10.0 raster_3.6-20
[17] withr_2.5.0 sp_1.6-0 gridExtra_2.3 tidyselect_1.2.0
[21] compiler_4.2.1 cli_3.6.1 Biobase_2.58.0 DelayedArray_0.24.0
[25] scales_1.2.1 nnls_1.4 rappdirs_0.3.3 systemfonts_1.0.4
[29] digest_0.6.31 tiff_0.1-11 SpatialExperiment_1.8.1 fftwtools_0.9-11
[33] svglite_2.1.1 rmarkdown_2.20 R.utils_2.12.2 XVector_0.38.0
[37] jpeg_0.1-10 pkgconfig_2.0.3 htmltools_0.5.5 sparseMatrixStats_1.10.0
[41] MatrixGenerics_1.10.0 fastmap_1.1.1 limma_3.54.2 htmlwidgets_1.6.2
[45] rlang_1.1.0 rstudioapi_0.14 shiny_1.7.4 DelayedMatrixStats_1.20.0
[49] generics_0.1.3 jsonlite_1.8.4 BiocParallel_1.32.6 dplyr_1.1.1
[53] R.oo_1.25.0 RCurl_1.98-1.10 magrittr_2.0.3 GenomeInfoDbData_1.2.9
[57] scuttle_1.8.4 Rcpp_1.0.10 ggbeeswarm_0.7.1 munsell_0.5.0
[61] S4Vectors_0.36.2 Rhdf5lib_1.20.0 fansi_1.0.4 viridis_0.6.2
[65] abind_1.4-5 lifecycle_1.0.3 R.methodsS3_1.8.2 terra_1.7-18
[69] yaml_2.3.7 edgeR_3.40.2 SummarizedExperiment_1.28.0 zlibbioc_1.44.0
[73] rhdf5_2.42.0 grid_4.2.1 parallel_4.2.1 promises_1.2.0.1
[77] dqrng_0.3.0 shinydashboard_0.7.2 lattice_0.20-45 beachmat_2.14.0
[81] locfit_1.5-9.7 magick_2.7.4 knitr_1.42 cytomapper_1.10.1
[85] pillar_1.9.0 GenomicRanges_1.50.2 rjson_0.2.21 codetools_0.2-19
[89] stats4_4.2.1 glue_1.6.2 evaluate_0.20 png_0.1-8
[93] vctrs_0.6.1 httpuv_1.6.9 gtable_0.3.3 ggplot2_3.4.1
[97] xfun_0.38 DropletUtils_1.18.1 mime_0.12 xtable_1.8-4
[101] later_1.3.0 viridisLite_0.4.1 SingleCellExperiment_1.20.1 tibble_3.2.1
[105] beeswarm_0.4.0 IRanges_2.32.0 ellipsis_0.3.2 here_1.0.1

[wangqiwei313]

Yea, I recently came across the same issue, I also tried other versions of this package, the R session always crashes inexplicable.